[R-SIG-Mac] XCode / gcc / R compatibility issues on Yosemite with XCode 7 and on El Capitan

[Prof Brian Ripley]

On 08/10/2015 02:37, Simon Urbanek wrote:
> Jenny,
>
> I suspect you may not have the correct information. The CRAN Mavericks binary of R is not built with gcc, it's actually build using Apple clang and we're neither using nor requiring homebrew, so most of what you are describing doesn't make sense to me. I have tested Xcode 7 with the gfortran-4.8 we supply and it works just fine on 10.11 (tested on Hmisc). I have only 10.6, 10.9 and 10.11 so I can't check 10.10, but I would certainly recommend building on 10.9 with Xcode 6 for compatibility (that's what we do for CRAN). If you don't care about binary compatibility then Xcode 7 on 10.11 is fine (FWIW Hmisc package compiled on 10.11 actually works for me on 10.9 so it could even be that you may get away with using 10.11 if you don't use system dependencies with higher versions).

It also works for me on 10.10.  If the 'Command Line Tools OS X 10 for 
Xcode 7' Apple package is installed on 10.10 (specifically file 
http://adcdownload.apple.com/Developer_Tools/Command_Line_Tools_OS_X_10.10_for_Xcode_7/Command_Line_Tools_OS_X_10.10_for_Xcode_7.dmg), 
it installs

% clang --version
Apple LLVM version 7.0.0 (clang-700.0.74)
Target: x86_64-apple-darwin14.5.0

hence targets OS X 10.10 aka Darwin 14.  My 10.10 machine does not have 
Xcode installed, only the CLT: you do not need Xcode's SDKs to compile R 
nor any CRAN package.  (You do need Xcode to compile R.app.)

For Fortran on Yosemite/El Capitan I use the gfortran 5.2 build at the 
sites given in the current R-admin manual ('Other builds of gfortran are 
available: see https://gcc.gnu.org/wiki/GFortranBinaries and 
http://coudert.name/software.html').  My recollection is that the 
'gfortran-4.8 for Mavericks' on r.research.att.com does compile all but 
one of the CRAN packages on Yosemite (SWATmodel which compiles 
executables from Fortran code), in some cases with warnings.

Note that any recent(ish) build of gfortran will have dynamic 
libgfortran and libquadmath libraries, and installations of most 
Fortran-using packages will link to these.  So you either need to 
install those libraries on all the machines or arrange for the packages 
you distribute to point to the copies in the CRAN build (in R_HOME/lib) 
as is done for the CRAN binary packages.  (I believe they are 
post-processed by 
https://svn.r-project.org/R-dev-web/trunk/CRAN/QA/Simon/packages/1.fixr 
.)  My recollection is that a very few packages also link to libgcc_s, 
also in R_HOME/lib.


> Cheers,
> Simon
>
>
>> On Oct 7, 2015, at 10:47 AM, Jenny Brown <jennybrown8 at gmail.com> wrote:
>>
>> I am maintaining R installations and packages for a large number of OS X
>> machines.  A recent change from Apple is making the R installation more
>> awkward, and I'm trying to determine the best path forward with minimal
>> maintenance headaches.
>>
>>
>> Recently, XCode 7's release on Yosemite 10.10 broke compilation of "brew
>> install --with-fortran gcc48" which is a pre-requisite for compiling third
>> party R packages that use fortran.  (XCode 7 eliminates the 10.9 and 10.10
>> SDKs and only provides 10.11 which is El Capitan's... so even though XCode
>> 7 installs on Yosemite, it can not build for Yosemite, which causes gcc
>> trouble.  Lots of opensource devs are commenting on this on various
>> projects.)
>>
>> It appears that the binary installs of R for OS X (3.1 through 3.2.2) were
>> all built against gcc 4.8.  I've discovered that gcc 5.2 builds properly on
>> Yosemite, even with XCode 7, and R can be compiled with gcc 5.2.
>>
>> However, even the latest R (3.2.2) on cran.rstudio.com appears to be built
>> by default with gcc 4.8 -- are there plans to move to gcc 5.2?  Presumably
>> the breakage I'm seeing where gcc 4.8 can't use the xcode 7 10.11 SDK would
>> also occur on El Capitan, so gcc 5.2 would be a necessary upgrade there too.
>>
>> Right now my choices for getting R to work with my third-party fortran
>> packages appear to be: manually downgrade xcode to 6.4 for Yosemite; or,
>> maintain my own compilation of R against gcc 5.2, for each of Yosemite and
>> El Capitan.  Both have their downsides, and I hope to be able to return to
>> the normal public binary R distribution sooner rather than later.
>>
>> What's on the roadmap for upcoming upgrades and compatibility?  Thanks.
>>
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>>
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-- 
Brian D. Ripley,                  ripley at stats.ox.ac.uk
Emeritus Professor of Applied Statistics, University of Oxford
1 South Parks Road, Oxford OX1 3TG, UK